diff CADDSuite-1.6/changelog.txt @ 10:eda78e0f5df6 draft default tip

Deleted selected files

--- a/CADDSuite-1.6/changelog.txt	Sat Dec 15 13:16:40 2012 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,104 +0,0 @@
-Version 1.6, 12-15-2012:
-	- Enhanced SurfaceMatcher; included correlation contributions for matching interior of binding pockets onto each other.
-	- Enhanced calculation of topological similarities.
-
-Version 1.5, 07-18-2012:
-	- Changed scoring function to include greatly improved solvation term !!!
-	- Added SurfaceMatcher. It finds the best superposition of two binding pocket surfaces using FFT !!
-	- Added PocketCutter, which allows to cut receptor atoms contributing to the SES of the binding pocket of a receptor. This output can then be used with SurfaceMatcher.
-	- Added k-mean clustering to MolDB
-	- For DBExporter and similarity search, allow to set threshold for max. desired molecules per query mol
-	- Allow to filter compound library by vendor name using DBExporter
-	- Allow to restrict similarity search to molecules with molecular weigth similar to the one of query molecule
-	- Added diversity criteria to DB similarity search and to MolFilter
-	- Optional automatic detection of ref. ligand (using largest heterosystem) added to PDBCutter
-	- PDBCutter can now also download ligand sdf with correct topology from PDB server instead just writing a pdb with unkown bond orders
-	- Adapted default penalty value set by SpatialConstraintDefiner and PocketDetector 
-
-Version 1.1, 01-10-2012:
-	- Eradicated use of external tool 'tar'. ScoreGridSets are now compressed using boost's gzip support. Multiple ScoreGridSets are automatically. concatenated and saved as one gzipped file
-	- Added default atom type for grid calculation
-	- Fixed default state of galaxy check-boxes
-	- Some small fixes for g++ 4.6
-	- Changed some default output formats of many tools to mol2.gz. This will only have an effect if _no_ valid file extension is specified.
-	- Gave some more tools the ability to delete their input file after sucessful execution
-	- The last two points together allow to reduce required disk space for common docking pipeline by about 95%.
-
-Version 1.0.1, 11-06-2011:
-	- In WaterFinder, remove existing water hydrogens before protonating and optimizing water molecules
-	- Fixed a parameter-related regression in IMGDock that led to the accidental use of non grid-based scoring functions
-	- Display meaningful error if automatic QSAR model creation is attempted with data not containing any response variables
-
-Version 1.0, 11-04-2011:
-	- Added support for advanced parameters and parameter sections
-	- Added some missing 'supported_formats' and 'tool_category' tags
-	- Fixed tar compression on Mac
-	- Fix for use of libsvm 3.1
-	- Fix for use of created release packages on MacOS 10.7
-	- Added missing flag to MolPredictor.
-
-Version 0.9.6, 08-20-2011:
-	- MolFilter: Use union of SMARTS matches instead of intersection
-	- Support for reading and writing compressed molecule files (*.gz)
-	- Added optional parameter for output log-file to DBImporter
-	- Added flag for disabling uniqueness-check to LigCheck
-	- mol2-files: disabled gaff atom-typing for speed-up
-	- drf-files: automatically add new protein-conformations
-	- Ligand3DGenerator: disable fallback-use of openbabel-UFF force field since it turned out to be unstable
-	- InputReader: made sure to always calculate correct set of features
-	- Fixed a nan problem during centering of QSAR data
-
-Version 0.9.5, 07-12-2011:
-	- Let rescoring search for correct LigCheck molecule property-tags
-	- Indicate optional parameters in galaxy interface
-	- Fixed compilation with disabled QuEasyViz
-	- Added missing gnuplot data file to release archive
-	- Set some default values for flags for use in GUIs
-	- Clarified EvenSplit docu
-
-Version 0.9.4, 06-27-2011:
-	- Fixed tool-startup script for pathes containing whitespaces
-	- New tool SpatialConstraintDefiner
-	- New tool InteractionConstraintDefiner
-	- Removed superficial pathes from startup-script
-	- Slight change in ParamFile format (i.e. the files written with -write_par)
-	- Renamed IMeedyDock to IMGDock
-
-Version 0.9.3, 05-30-2011:
-	- Split Rescorer into 3 tools: SimpleRescorer, TaGRes-train, TaGRes (Target-Specific Grid-Rescoring)
-	- Allow to optionally specify output filenames to LigandFileSplitter
-	- Fixed creation of galaxy-scripts for tools with inputfile-lists
-	- Fixed creation of galaxy-scripts for Converter and DockResultMerger
-	- Automatically create and add all files necessary for integration of CADDSuite into Galaxy to the makeself archive
-	- New tool MolFilter
-	- Fixed some gnuplot issues
-	- Added PDBDownload tool
-	- Slight change of format of ParamFile
-	- Added some missing tool-manuals
-	- Disable B-factor check for hydrogens in ProteinCheck
-	- Added safeguards to several tools
-	- Automatically delete existing hydrogens from BALL-system before protonation is done by ProteinProtonator
-	- Fixed reading of mulitple ScoreGridSets (for cases when no ini-file is used)
-	- Simplified use of VendorFinder by allowing to set all db-parameters on the command-line (instead of using ini-file)
-	- Enhanced several tool manuals
-	- Let tools register their category (e.g. Preparation, Docking, etc.). Write and read information about this category to/from ParamFiles.
-
-Version 0.9.2, 05-17-2011:
-	- Speed-up of ob-mol generation
-	- Support build on Windows
-	- ProteinCheck now generates protein-quality report as pdf
-	- Added info about mandatory parameters and parameter-restrictions to parameter xml-file
-	- Simplified use of DBImporter+DBExporter by allowing to set all db-parameters on the command-line (instead of using ini-file)
-	- Simplified use of some other tools by merging several flags into one string-parameter that has restrictions.
-	- New tool MolDepict. It generates structure diagrams for small molecules by using openbabel's svg-writer and merges them to one pdf-file (3 on 5).
-	- Allow to create makeself-archive containing CADDSuite, all necessary contrib-libs, data-files and install-script
-	- Write information about supported file-formats to parameter xml-file
-	- new tool ProteinProtonator
-	- new tool Ligand3DGenerator
-	- new tool GalaxyConfigGenerator
-	- allow to open file that do not have an extension (by searching for format-specific keywords)
-
-Version 0.9.1, 04-12-2011:
-	- All tools now write a manual text to cout as well as to parameter xml-file (as generated by -write_par)
-
-Version 0.9